TABLE 1.
Comparison of algorithms for global rigid body modeling
| DIMFOM | GLOBSYMM | SASREF | BUNCH | |
|---|---|---|---|---|
| Objects | Homo- and heterodimers | Symmetric oligomers with one monomer per asymmetric part | Macromolecular complexes | Multidomain proteins; complexes of subunits with missing fragments |
| Multiple data sets fitting | No | No | Yes | Yes |
| Maximum number of independent rigid bodies | 2 | 1 | 10 | 10 |
| Symmetry | P1, P2 | P2–P6, P222–P62 | P1–P6, P222–P62 | P1–P6, P222–P62 |
| Minimization method | Rolling on the surface | Global grid search | Simulated annealing | Simulated annealing |
| Constraints | Symmetry, interconnectivity | Symmetry, interconnectivity | Symmetry | Symmetry, interconnectivity |
| Restraints | — | Steric clashes, pair contacts | Interconnectivity, steric clashes, pair contacts | Compactness, steric clashes, and bond/dihedral angles in DR loops |
| Number of target function evaluations/CPU, min | 4000/0.5 | 15,000/3 | 1.2 × 105/50 | 3 × 105/80 |